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| kanzure | hmph | 07:52 |
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| kanzure | fenn: why bother with sequencing with FISSEQ and proten expression labeling stuff, if you are already placing the tissue slice in front of a microscope anyway? you might as well do imaging, not sequencing. | 08:27 |
| kanzure | for connections i think sequencing is still required. | 08:27 |
| kanzure | https://openaps.org/ "open artificial pancreas project" | 08:29 |
| kanzure | https://openaps.org/reference-design/ | 08:29 |
| kanzure | https://github.com/openaps/openaps | 08:29 |
| kanzure | https://github.com/openaps/oref0 | 08:30 |
| CaptHindsight | I'm glad they chose the pancreas, the pancreas and the spleen tend to get overshadowed by other organs in the press | 08:53 |
| CaptHindsight | how many news articles feature the spleen? It tends to be heart, lungs and stomach | 08:54 |
| kanzure | .wik systematic evolution of ligands by exponential enrichment | 08:56 |
| yoleaux | "Systematic evolution of ligands by exponential enrichment (SELEX), also referred to as in vitro selection or in vitro evolution, is a combinatorial chemistry technique in molecular biology for producing oligonucleotides of either single-stranded DNA or RNA that specifically bind to a target ligand or ligands." — https://en.wikipedia.org/wiki/Systematic_evolution_of_ligands_by_exponential_enrichment | 08:56 |
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| streety | I thought that open pancreas project was started and run by diabetics - i.e. they're building a device they themselves want to use / are using | 09:09 |
| kanzure | here is a good overview of SELEX things http://www.medicinal-chemistry.org/files/harki/The%20Discovery%20of%20Protein-Targeting%20Aptamers%20by%20SELEX.pdf | 09:11 |
| kanzure | "cell-SELEX" i wonder if this is for cell surface property selection, or if this is something else.. | 09:13 |
| kanzure | another overview http://www.trilinkbiotech.com/tech/selex.asp | 09:17 |
| kanzure | peptide sequencing still works, right? we could modify a ribosome to print random amino acid chains instead of looking at RNA. the goal would be to select for ribosomes that print really long proteins. and then later the goal would be to select for ribosomes that are more controllable by human influence or human-generated signals. (this is an alternative to the idea of using a library of 64 synthetases and an evolved ribosome that binds ... | 09:21 |
| kanzure | ... to whatever synthetase we give it). | 09:21 |
| CaptHindsight | kanzure: for some reason the inkjet DNA printer is suddenly getting interest yet the paper is from 2004 | 09:23 |
| kanzure | https://www.google.com/search?q=site%3Aigem.org+SELEX | 09:24 |
| kanzure | CaptHindsight: POSAM? yeah i think it has always been popular :). | 09:24 |
| CaptHindsight | kanzure: maybe in here but not outside | 09:24 |
| CaptHindsight | the ChinaCo flatbad inkjets are made too crappy, like most reprap style printers... | 09:25 |
| CaptHindsight | so I can't start with those and expand, cheap bastards | 09:26 |
| kanzure | there's probably an inkjet manufacturer that would be interested in getting into biotech or having their system at the heart of a biotech revolution, who's in your rolodex? :P | 09:28 |
| CaptHindsight | I hope that they don't cheap out copying the design I give them | 09:28 |
| CaptHindsight | me | 09:28 |
| CaptHindsight | I know them all. They are clueless when it comes to materials deposition | 09:29 |
| CaptHindsight | they all want the graphics arts applications with $5/L inks that sell for $4k/L | 09:29 |
| kanzure | do they recognize their relevance to industrial applications? | 09:30 |
| CaptHindsight | they are money driven, if they made a POSAM it would be $100K and the fluids would be $10K/g vs $1k/g | 09:30 |
| CaptHindsight | there are the greediest and most controlling types that you have met | 09:31 |
| CaptHindsight | that's why the inkjet industry is so secretive | 09:32 |
| kanzure | "Gilead currently holds the patent rights to the SELEX technology and has licensed it to Archemix, who is using the technology to develop pharmaceutical applications for aptamers. Archemix has sublicensed this technology to NOXXON, who is using it for the development of their Spiegelmer® technology." | 09:32 |
| CaptHindsight | NDA's for everything | 09:33 |
| kanzure | hah someone patented SELEX. wonderful.... sigh. | 09:33 |
| CaptHindsight | kanzure: which countries advertise medical tourism and not enforce the US patent system? | 09:34 |
| CaptHindsight | or maybe do so less than others | 09:34 |
| kanzure | US patent system is worldwide enforced through an evil organization called WIPO | 09:34 |
| CaptHindsight | tell that to China | 09:34 |
| kanzure | https://en.wikipedia.org/wiki/World_Intellectual_Property_Organization | 09:34 |
| kanzure | china uses WIPO for their own patents | 09:35 |
| CaptHindsight | heh | 09:35 |
| CaptHindsight | well grasshopper, you have much to discover | 09:35 |
| kanzure | fightaging.org was organizing a medical tourism initiative, he had picked a number of candidate countries | 09:35 |
| CaptHindsight | it's selective enforcement | 09:35 |
| kanzure | china can turn a blindeye to some things but i get the sense that it's more related to paying off the right people, rather than china being OK with things. | 09:35 |
| kanzure | anyway, reason@fightaging.org would be the person to ask regarding medical tourism | 09:36 |
| CaptHindsight | or if your project/company is guberment funded | 09:36 |
| kanzure | apparently he moved to austin, texas but we've never met each other. he is trying to remain anonymous. i think i'll get him eventually. | 09:36 |
| CaptHindsight | believe me they are OK with some things | 09:37 |
| CaptHindsight | most authors apply for the patent right before publishing their papers | 09:38 |
| CaptHindsight | why I often see the patent awarded <1 year after publishing | 09:39 |
| CaptHindsight | "hey here's what we found, loo at this" but "F-You we patented it" | 09:39 |
| CaptHindsight | loo/look | 09:40 |
| streety | the patents on SELEX look to be over 20 years old | 09:40 |
| CaptHindsight | have any open source not for profit projects ever been sued for patent infringement? | 09:41 |
| kanzure | where is mindspillage, she would have good answers | 09:42 |
| CaptHindsight | I'd focus on getting things to actually work | 09:45 |
| CaptHindsight | negotiate later | 09:46 |
| CaptHindsight | it's easy to talk about something for several years without getting anything done | 09:47 |
| chris_99 | .title http://www.bbc.co.uk/news/technology-36711994 | 10:15 |
| yoleaux | The DIY diabetes kit that's keeping us alive - BBC News | 10:15 |
| CaptHindsight | yeah #wearenotwaiting, I thought we'd be way ahead of where we are now by 2000 | 10:17 |
| CaptHindsight | I need to patent the nano-usb connector | 10:19 |
| CaptHindsight | what's a good com port for a nanoscale device to connect to a PC? | 10:20 |
| CaptHindsight | what are the most efficient ways to get data in and out of a hybrid nanoscale oligo factory? | 10:22 |
| CaptHindsight | say we drop an 8-bit micro into a cell with a few K or RAM, what's the best way to communicate with it using a PC? | 10:23 |
| CaptHindsight | or/of | 10:24 |
| kanzure | probably radio, light, stuff like that | 10:24 |
| kanzure | long-term, the biologists seem to think that we will be using DNA to send messages from cells | 10:25 |
| kanzure | for example, the other day in here i mentioned someone's proposal to have an array of nanopore dna sequencing devices at the human heart to read any dna messages directly from the bloodstream | 10:25 |
| CaptHindsight | yes, but making it practical | 10:26 |
| CaptHindsight | the heart is a good central point but the cells are rushing through it pretty quickly | 10:26 |
| CaptHindsight | and how do you read a ton of them at once? | 10:26 |
| kanzure | huge array of nanopores for sequencing | 10:27 |
| kanzure | if you don't capture the molecule no big deal, it will come back around eventually | 10:27 |
| CaptHindsight | I guess I'll have to work on the practical end | 10:28 |
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| xentrac | CaptHindsight: one of the things the Berkeley Motes folks did was modulate a retroreflector for communication | 10:41 |
| xentrac | so you would shine a light at a mote with, say, 1mW of light, and get back something like a 100μW signal from the mote, which was spending nW power levels moving a mirror back and forth to make and break a corner reflector | 10:42 |
| kanzure | another dna synthesis proposal https://groups.google.com/d/msg/enzymaticsynthesis/8Upr8bPY-7I/R9X08u-oBwAJ | 10:59 |
| fenn | kanzure: i guess you missed the point of FISSEQ/aptamer idea - it's not for sequencing, it's so you can do a whole lot of different stains in a single image. arbitrarily many, instead of just two or three | 11:13 |
| fenn | IRDA for nanobot comms lol | 11:18 |
| fenn | i knew i was saving that PDA for something | 11:18 |
| CaptHindsight | xentrac: recall the data rate? | 11:18 |
| fenn | it's just a serial port | 11:18 |
| kanzure | FISSEQ was about sequencing, not staining :) | 11:19 |
| fenn | 20 kbit | 11:20 |
| kanzure | without FISSEQ you can already do lots of cycles of antibody staining, imaging and washing | 11:20 |
| fenn | .title info.iet.unipi.it/~anastasi/papers/mswim04.pdf | 11:20 |
| fenn | bah | 11:20 |
| yoleaux | fenn: Sorry, that doesn't appear to be an HTML page. | 11:20 |
| fenn | "Performance Measurements of Motes Sensor Networks" | 11:21 |
| xentrac | no | 11:21 |
| fenn | oh maybe 250 kbit | 11:21 |
| kanzure | if you are doing in situ sequencing with FISSEQ then you have tissue in front of a microscope, you might as well do protein expression labeling and imaging since you have the microscope there anyway. i guess you could argue "just collect all the DNA that stuck around, and sequence it later" which is nice i guess, or you could argue "nobody's got time for multiple rounds of staining and washing" and "multiple rounds is too damaging to ... | 11:23 |
| kanzure | ... tissue" which are true things... | 11:23 |
| fenn | kanzure the protein and RNA are not going to be in the same place | 11:24 |
| kanzure | hm? the aptamer is supposed to find the protein and attach to the protein. | 11:24 |
| fenn | yes | 11:25 |
| fenn | uh, nevermind, i thought you meant something else by "expression" | 11:25 |
| kanzure | "expressed proteins" | 11:26 |
| kanzure | (rather than "gene expression", which is apparently what lots of other people are interested in) | 11:26 |
| fenn | CaptHindsight: "CCR reflectivity can be modulated at bit rates up to 10 kbps" | 11:28 |
| fenn | from http://robotics.eecs.berkeley.edu/~pister/publications/1998/smartdust_comm_memo.pdf | 11:28 |
| kanzure | marblestone did an okay writeup of a lot of potential "chips in cells" stuff | 11:29 |
| fenn | corner cube retroreflector is for long distance communication though, you could do a lot faster with just an LED | 11:30 |
| fenn | assuming you have the power to run it | 11:31 |
| xentrac | the retroreflector thing is for avoiding the need to have the power to run it | 11:44 |
| xentrac | I imagine you could modulate a mechanical mirror at several MHz with enough power too | 11:45 |
| xentrac | although of course you can modulate many LEDs at hundreds of MHz | 11:45 |
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| kanzure | http://biology.stackexchange.com/questions/19316/first-rna-polymerase-mrna | 13:59 |
| kanzure | "Johnston et al. (2001) took this experiment even further: starting with a pool of slightly mutated ribozyme ligases developed in a previous SELEX experiment, they were able to generate a ribozyme polymerase. This polymerase was able to catalyze the addition of nucleotides to a growing oligonucleotide chain up to 14 bases long and based off of an RNA template. The polymerase was also quite accurate." | 14:01 |
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| kanzure | "RNA-catalyzed RNA polymerization: Accurate and general RNA-templated primer extension" http://fab.cba.mit.edu/classes/S62.12/docs/Bartel_RNA.pdf | 14:16 |
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| kanzure | .wik polynucleotide phosphorylase | 14:29 |
| yoleaux | "Polynucleotide Phosphorylase (PNPase) is a bifunctional enzyme with a phosphorolytic 3' to 5' exoribonuclease activity and a 3'-terminal oligonucleotide polymerase activity. That is, it dismantles the RNA chain starting at the 3' end and working toward the 5' end. It also synthesizes long, highly heteropolymeric tails in vivo." — https://en.wikipedia.org/wiki/Polynucleotide_phosphorylase | 14:29 |
| kanzure | "Discovered by Ochoa in 1951, the RNA-polymerization activity of PNPase was initially believed to be responsible for DNA-dependent synthesis of messenger RNA, a notion that got disproved by the late 1950s (http://www.jbc.org/content/281/15/e12.full.pdf). | 14:29 |
| kanzure | " | 14:29 |
| kanzure | "The same abbreviation (PNPase) is also used for another, otherwise unrelated enzyme, Purine nucleoside phosphorylase." | 14:30 |
| kanzure | ugh | 14:30 |
| kanzure | "Polyribonucleotide phosphorylase is a double-stranded DNA-binding protein." http://www.ncbi.nlm.nih.gov/pubmed/9502433 | 14:33 |
| kanzure | "[...] The PNPase possesses two enzymatic activities, namely 3'-5' processive exoribonuclease activity and 5'-3' RNA polymerase activity" | 14:33 |
| kanzure | "plastid-encoded polymerase" "nucleus-encoded polymerase" "... Given that DNA and RNA polymerases both carry out template-dependent nucleotide polymerization, it might be expected that the two types of enzymes would be structurally related. However, x-ray crystallographic studies of both types of enzymes reveal that, other than containing a critical Mg2+ ion at the catalytic site, they are virtually unrelated to each other; indeed ... | 14:37 |
| kanzure | ... template-dependent nucleotide polymerizing enzymes seem to have arisen independently twice during the early evolution of cells. One lineage led to the modern DNA Polymerases and reverse transcriptases, as well as to a few single-subunit RNA polymerases from viruses. The other lineage formed all of the modern cellular RNA polymerases." | 14:37 |
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| kanzure | "New Nonnucleoside Substrates for Terminal Deoxynucleotidyl Transferase: Synthesis and Dependence of Substrate Properties on Structure" (2005) | 16:23 |
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| kanzure | church writes perl :\ some of his scripts are included in various patents | 16:28 |
| ebowden_ | Church is love, Church is life. | 16:28 |
| kanzure | "Genetically encoding photoswitchable click amino acids in Escherichia coli and mammalian cells" http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4051619/ (2015) | 16:38 |
| kanzure | "In situ formation of an azo bridge on proteins controllable by visible light" http://pubs.acs.org/doi/abs/10.1021/jacs.5b06234?journalCode=jacsat | 16:39 |
| kanzure | "Small molecule photoswitches could complement protein-based switches by mitigating potential interference and affording high specificity for modulation sites. However, genetic encodability and responsiveness to nonultraviolet light, two desired properties possessed by protein photoswitches, are challenging to be engineered into small molecule photoswitches. Here we developed a small molecule photoswitch that can be genetically installed ... | 16:40 |
| kanzure | ... onto proteins in situ and controlled by visible light. A pentafluoro azobenzene-based photoswitchable click amino acid (F-PSCaa) was designed to isomerize in response to visible light. After genetic incorporation into proteins via the expansion of the genetic code, F-PSCaa reacts with a nearby cysteine within the protein generating an azo bridge in situ. The resultant bridge is switchable by visible light and allows conformation and ... | 16:40 |
| kanzure | ... binding of CaM to be regulated by such light. This photoswitch should prove valuable in optobiology for its minimal interference, site flexibility, genetic encodability, and response to the more biocompatible visible light." | 16:40 |
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| kanzure | and here is one that uses spiropyran instead of azobenzene https://www.weizmann.ac.il/Organic_Chemistry/Rafal/pub/Noncovalent_Interactions_with_Proteins_Modify%20_the_Physicochemical_Properties_of_a_Molecular_Switch.pdf | 16:48 |
| kanzure | although this one does not seem to use artificial amino acids | 16:48 |
| kanzure | "Photosensitive GFP mutants containing an azobenzene unnatural amino acid" http://www.sciencedirect.com/science/article/pii/S0960894X14013432 | 16:49 |
| kanzure | using an artificial amino acid seems like a much better technique compared to using spiropyran or azobenzene in a dnazyme or ribozyme like from "Light-driven DNA nanomachine with a photoresponsive molecular engine" http://pubs.acs.org/doi/abs/10.1021/ar400308f | 16:50 |
| kanzure | or like from "Photoswitch nucleic acid catalytic activity by regulating topological structure with a universal supraphotoswitch" http://pubs.acs.org/doi/abs/10.1021/sb300120n | 16:50 |
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| kanzure | "Rewiring Multidomain Protein Switches: Transforming a Fluorescent Zn2+ Sensor into a Light-Responsive Zn2+ Binding Protein" (ligand activity modulated by photoswitching, or er, binding activity only functional under illumination, rather) | 16:58 |
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| kanzure | "Azobenzene photoswitching without ultraviolet light" http://2014.igem.org/wiki/images/0/0e/Technion-Israel-Azobenzene.pdf (2011) (supplementary info) | 17:12 |
| kanzure | "Most azobenzene-based photoswitches use UV light for photoisomerization. This can limit their application in biological systems, where UV light can trigger unwanted responses, including cellular apoptosis. We have found that substitution of all four ortho positions with methoxy groups in an amidoazobenzene derivative leads to a substantial (~35 nm) red shift of the n-π* band of the trans isomer, separating it from the cis n-π* ... | 17:12 |
| kanzure | ... transition. This red shift makes trans-to-cis photoswitching possible using green light (530-560 nm). The cis state is thermally stable with a half-life of ~2.4 days in the dark in aqueous solution. Reverse (cis-to-trans) photoswitching can be accomplished with blue light (460 nm), so bidirectional photoswitching between thermally stable isomers is possible without using UV light at all." | 17:12 |
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| CaptHindsight | hhmmm no open source CGM Continuous Glucose Monitor | 17:29 |
| CaptHindsight | need an open biosensor project | 17:33 |
| CaptHindsight | jesus , everything needs to be built | 17:36 |
| CaptHindsight | has anyone actually built anything other than some software for an Rpi? | 17:37 |
| kanzure | lots of people use the gpio pins | 17:51 |
| kanzure | "A general method for regulating protein stability with light" http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3906921/ (2013) | 18:05 |
| kanzure | "We here describe a novel genetically encoded protein domain that is degraded upon exposure to non-toxic blue light. We demonstrate that fusion proteins containing this domain are rapidly degraded in cultured cells and in zebrafish upon illumination." | 18:05 |
| kanzure | degradation is a little bit overkill but i guess that's better than nothing. and it's a protein domain so that's nice.. | 18:05 |
| kanzure | "Blue-Light Inducible Degradation (B-LID) domain" | 18:06 |
| yashgaroth | only works intracellularly, mediated by the proteasome | 18:08 |
| kanzure | oh. | 18:10 |
| kanzure | and the azobenzene unnatural amino acid? are you going to tell me santa claus isn't real, next? | 18:10 |
| yashgaroth | nah that's probably fine | 18:11 |
| CaptHindsight | benzos are often used in radiation/light reactive applications | 18:14 |
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| kanzure | yex the reason why it's useful here is because someone put it into an amino acid and an expanded genetic alphabet | 18:15 |
| kanzure | so a genome can specify, through genetics, that a certain amino acid in a certain protein should be responsive to light, or be light-switchable | 18:16 |
| kanzure | which is useful for an optically controlled polymerase | 18:16 |
| CaptHindsight | there's a shitload of photoreactive things you can do to oligos | 18:16 |
| CaptHindsight | I don't think the bio people spend much time looking into what they do in industrial applications | 18:17 |
| kanzure | yes yesterday i pointed out a few papers where they use azobenzene and spiropyran and friends to make dnazymes and ribozymes that undergo movement in response to optical stimulation | 18:17 |
| CaptHindsight | they should probably have lunch with the industrial chemists some time :) | 18:17 |
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| kanzure | yeah the photopolymer/photoresin materials people seem to get involved in lots of deeply weird thngs | 18:22 |
| kanzure | and then there's dye stuff... | 18:22 |
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| kanzure | non-covalently bound light-controlled inhibitor of a protein's catalytic activity domain http://onlinelibrary.wiley.com/doi/10.1002/anie.201307207/full (this seems to be a free-floating inhibitor) | 19:08 |
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| kanzure | "Methods of storing information using nucleic acids" https://patents.google.com/patent/US20150269313A1/en | 19:14 |
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| kanzure | some sort of academic paper recommendation engine thing https://github.com/titipata/science_concierge | 19:27 |
| kanzure | from kording lab | 19:27 |
| kanzure | "sciencestein" | 19:27 |
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| nildicit | any thoughts on http://www.transhumanpolitics.com/ ? | 19:51 |
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| kanzure | waste of time; better to build things. | 20:07 |
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| nmz787 | damn, for half a second I read PMPase and heard it in my head as 'pimp-ase'... but then re-read and saw it was PNPase :( | 20:45 |
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| nildicit | kanzure, how are the political motives injected into the creation of things a waste of time tho | 21:01 |
| nmz787 | nildicit: I don't think kanzure gets how many people out there are easily swayed by a free meal to ensue violence and/or property destruction | 21:06 |
| nmz787 | and thus the need to educate them and get them on 'our side' | 21:07 |
| nmz787 | (even though it seems damn obvious to us) | 21:07 |
| nmz787 | nildicit: in general politics is basically salesmanship and communications between tribes... and being a salesman sucks | 21:07 |
| nmz787 | I work in a tech company and was just recently told I need to sell ideas to higher-ups... because even though we're all tech folks, they need sold to because shit isn't obvious | 21:08 |
| nildicit | I remember an immortallife article questioning whether or not "deathism" is a meme. | 21:09 |
| nildicit | Those were dark times | 21:09 |
| nmz787 | knowledge in humans doesn't seem to be able to be wide and deep for many people | 21:09 |
| nildicit | engineers don't like politics, I know. | 21:10 |
| nildicit | I've been reading into the history of the transhumanist political landscape and it's weird | 21:10 |
| nildicit | things have definitely changed in the past four/five years too | 21:11 |
| nildicit | The Transhumanist National Commitee was formed in response to the Zoltan Istvan's illegitimate party and campaign for instance | 21:13 |
| kanzure | i am going to ban you | 21:13 |
| kanzure | this is an immense waste of time | 21:13 |
| nildicit | I'm not even trolling, kanzure | 21:13 |
| nildicit | You still haven't answered my question | 21:14 |
| kanzure | i know. i don't care. it's still a waste of time. get the fuck out. | 21:14 |
| * nildicit goes back to idling | 21:15 | |
| kanzure | only reason why this place is still around is because i keep murdering anyone who even hints at politicizing any of this shit; i will absolutely disembowel you and drown you in a mixture of your own blood vomit piss. | 21:15 |
| kanzure | thanks. | 21:15 |
| nildicit | No wonder this place is pretty dead. | 21:16 |
| ebowden_ | Not really. | 21:16 |
| ebowden_ | Lots of technical discussion. | 21:17 |
| ebowden_ | Oh, wait, nevermind. | 21:17 |
| ebowden_ | Not lots. | 21:17 |
| nildicit | My logs consist of more kanzure link/quoting than anything else tbh | 21:17 |
| nildicit | Not like that's a bad thing | 21:17 |
| nildicit | it's not | 21:17 |
| ebowden_ | kanzure, did that vetinary oncologist and complete troll, Lando-SpacePimp, get banned from this channel? | 21:19 |
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| kanzure | that was probably another channel | 21:22 |
| ebowden_ | Ah, ok. | 21:22 |
| ebowden_ | Yeah, I remember they were banned in a channel, just not which one it was. | 21:22 |
| ebowden_ | That one is actually a scientist, just also a troll. Apparently they earned a reputation of sorts, brought Surströmming to Food Friday at vet school. | 21:24 |
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| kanzure | http://www.aptagen.com/aptamer-index/aptamer-list.aspx | 21:45 |
| kanzure | fenn: you shoud have argued "the wash cycles probably don't work", it's a good reason to do aptamers + sequencing rather than microscopy imaging of colors. | 21:56 |
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| Th3_Prince | hey | 23:36 |
| Th3_Prince | what should i major in if I want to go into agi | 23:36 |
| chris_99 | hmm not sure, but you could look into computational neuroscience | 23:39 |
| Th3_Prince | eh | 23:39 |
| Th3_Prince | between physics | 23:39 |
| Th3_Prince | math | 23:39 |
| Th3_Prince | and compsci | 23:39 |
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| --- Log closed Sun Jul 17 00:00:59 2016 | ||
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